comparison tools/mira4_0/mira4_de_novo.xml @ 26:8aeb92e76159 draft

planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 4fbb738ddbc87132ca11dfaaaa38aa922ac87115-dirty

25:55ae131c5862

<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.8">
    <description>Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
    <requirements>
        <requirement type="binary">mira</requirement>
        <requirement type="binary">miraconvert</requirement>
        <requirement type="package" version="4.0.2">MIRA</requirement>

            <param name="job_quality" value="accurate" />
            <param name="technology" value="sanger" />
            <param name="type" value="none" />
            <param name="filenames" value="U13small_m.fastq" ftype="fastqsanger" />
            <param name="maf_wanted" value="true"/>
            <param name="bam_wanted" value="true"/>
            <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" />
            <output name="out_bam" file="empty_file.dat" compare="contains" />
            <!-- TODO: Suggest startswith as a compare method? -->
            <output name="out_maf" file="header.mira" compare="contains" />
            <output name="out_log" file="empty_file.dat" compare="contains" />
        </test>
        <!-- Simple assembly based on MIRA's minidemo/solexa1 example
             Note we're using just one repeat group,
             but two parameters within the repeat (filename, no pairing)
         -->

            <param name="type" value="none" />
            <param name="filenames" value="ecoli.fastq" ftype="fastqsanger" />
            <param name="maf_wanted" value="false"/>
            <param name="bam_wanted" value="false"/>
            <output name="out_fasta" file="ecoli.mira4_de_novo.fasta" ftype="fasta" />
            <output name="out_log" file="empty_file.dat" compare="contains" />
        </test>
    </tests>
    <help>

**What it does**

26:8aeb92e76159

<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.9">
    <description>Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
    <requirements>
        <requirement type="binary">mira</requirement>
        <requirement type="binary">miraconvert</requirement>
        <requirement type="package" version="4.0.2">MIRA</requirement>

            <param name="job_quality" value="accurate" />
            <param name="technology" value="sanger" />
            <param name="type" value="none" />
            <param name="filenames" value="U13small_m.fastq" ftype="fastqsanger" />
            <param name="maf_wanted" value="true"/>
            <param name="bam_wanted" value="false"/>
            <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" />
            <output name="out_maf" file="U13small_m.mira4_de_novo.mira" ftype="mira" />
            <output name="out_log" file="empty_file.dat" compare="contains" ftype="txt" />
        </test>
        <!-- Simple assembly based on MIRA's minidemo/solexa1 example
             Note we're using just one repeat group,
             but two parameters within the repeat (filename, no pairing)
         -->

            <param name="type" value="none" />
            <param name="filenames" value="ecoli.fastq" ftype="fastqsanger" />
            <param name="maf_wanted" value="false"/>
            <param name="bam_wanted" value="false"/>
            <output name="out_fasta" file="ecoli.mira4_de_novo.fasta" ftype="fasta" />
            <output name="out_log" file="empty_file.dat" compare="contains" ftype="txt" />
        </test>
    </tests>
    <help>

**What it does**